Biomaterial Database

pKa of adenine 2451 in the ribosomal peptidyl transferase center remains elusive. 2001

L Xiong, and N Polacek, and P Sander, and E C Böttger, and A Mankin

The universally conserved A2451 of 23S rRNA has been proposed to participate directly in the catalysis of peptide bond formation in the ribosomal peptidyl transferase center. An unusually high, near neutral, pKa of A2451 is a prerequisite for its action as a general acid-base catalyst. Increased reactivity of A2451 to dimethylsulfate (DMS) at pH 8.5 compared to pH 6.5 was taken as evidence that the pKa of this nucleotide falls within this pH range. Structural data suggested that the interaction between A2451 and G2447 in the ribosome is responsible for A2451 pKa perturbation. In contrast to expectation, our studies did not show pH dependence of A2451 dimethylsulfate modification in ribosomes of Thermus aquaticus and Mycobacterium smegmatis. Other rRNA regions, however, showed major alterations in DMS reactivity at pH 8.5 compared to pH 6.5, suggesting that conformational rearrangements in the structure of the large ribosomal subunit may occur upon the pH shift. The G2447U mutant of M. smegmatis was viable, indicating that the G2447-A2451 interaction is not critical for the ribosome function. We concluded that the proposed unusual pKa of A2451, if existing, may not be crucial for the ribosome activity and that the previously reported pH-dependent alterations in the DMS modification of A2451 do not necessarily reveal an unusual pKa of this nucleotide.

UI	MeSH Term	Description	Entries
D008969	Molecular Sequence Data	Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.	Sequence Data, Molecular,Molecular Sequencing Data,Data, Molecular Sequence,Data, Molecular Sequencing,Sequencing Data, Molecular
D009690	Nucleic Acid Conformation	The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape.	DNA Conformation,RNA Conformation,Conformation, DNA,Conformation, Nucleic Acid,Conformation, RNA,Conformations, DNA,Conformations, Nucleic Acid,Conformations, RNA,DNA Conformations,Nucleic Acid Conformations,RNA Conformations
D010458	Peptidyl Transferases	Acyltransferases that use AMINO ACYL TRNA as the amino acid donor in formation of a peptide bond. There are ribosomal and non-ribosomal peptidyltransferases.	Peptidyl Transferase,Peptidyl Translocase,Peptidyl Translocases,Peptidyltransferase,Transpeptidase,Transpeptidases,Peptidyltransferases,Transferase, Peptidyl,Transferases, Peptidyl,Translocase, Peptidyl,Translocases, Peptidyl
D000225	Adenine	A purine base and a fundamental unit of ADENINE NUCLEOTIDES.	Vitamin B 4,4, Vitamin B,B 4, Vitamin
D001483	Base Sequence	The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.	DNA Sequence,Nucleotide Sequence,RNA Sequence,DNA Sequences,Base Sequences,Nucleotide Sequences,RNA Sequences,Sequence, Base,Sequence, DNA,Sequence, Nucleotide,Sequence, RNA,Sequences, Base,Sequences, DNA,Sequences, Nucleotide,Sequences, RNA
D012270	Ribosomes	Multicomponent ribonucleoprotein structures found in the CYTOPLASM of all cells, and in MITOCHONDRIA, and PLASTIDS. They function in PROTEIN BIOSYNTHESIS via GENETIC TRANSLATION.	Ribosome
D012329	RNA, Bacterial	Ribonucleic acid in bacteria having regulatory and catalytic roles as well as involvement in protein synthesis.	Bacterial RNA
D012338	RNA, Ribosomal, 23S	Constituent of 50S subunit of prokaryotic ribosomes containing about 3200 nucleotides. 23S rRNA is involved in the initiation of polypeptide synthesis.	23S Ribosomal RNA,23S rRNA,RNA, 23S Ribosomal,Ribosomal RNA, 23S,rRNA, 23S
D013824	Thermus	Gram-negative aerobic rods found in warm water (40-79 degrees C) such as hot springs, hot water tanks, and thermally polluted rivers.
D020102	Mycobacterium smegmatis	A rapid-growing, nonphotochromogenic species of MYCOBACTERIUM originally isolated from human smegma and found also in soil and water. (From Dorland, 28th ed)